The Mozambique Channel is a conduit of trade wind-driven throughflow that is a key component of the Agulhas Current and Agulhas leakage, a flux of warm and salty water from the tropical Indo-Pacific to the Atlantic Ocean. Agulhas leakage is thought to modulate Atlantic meridional overturning circulation variability. Previous studies from the Cape Basin suggest that enhanced Agulhas leakage played an important role in accelerating glacial terminations. The southern African monsoon response to abrupt climate changes associated with meltwater-induced reorganizations of the North Atlantic meridional overturning circulation, and its impact on the Mozambique Channel throughflow and, by extension, on the Agulhas leakage is not well understood. Here we present a high-resolution 26,000 year-long hydroclimate record of northern Madagascar, a core region of the southern hemisphere monsoon domain, and a mixed layer temperature reconstruction using sediment cores collected from the runoff-influenced eastern Mozambique Channel. The record indicates precipitation increases centered at 11.7-12.5 thousand years before present (kyr BP), 14.5-19 kyr BP, 23-24 kyr BP, 25-26 kyr BP. Considering age model uncertainties, this is the first strong evidence for southern African monsoon strengthening in response to meltwater-induced northern high latitude climate instabilities during the Younger Dryas (YD), Heinrich Stadial 1 (HS1), HS2 and the HS-like event prior to HS2, in agreement with the results of transient climate simulations. Furthermore, our study shows a reversal of the mixed layer temperature gradient between the western and eastern Mozambique Channel during Heinrich event 1 (HE1). We posit that the gradient reversal indicates a weakening of the trade wind-driven South Equatorial Current and Mozambique Channel throughflow that likely weakened the Agulhas leakage, potentially creating a feedback that may have contributed to the sustained weakening of the AMOC during HE1 by reducing the amount of heat and salt leakage into the Atlantic.